This repo contains a number of Hail utility functions and scripts for the gnomAD project and the MacArthur lab. Load using:

from gnomad_hail.resources import *
from gnomad_hail.utils import *
from gnomad_hail.slack_utils import *

Resource map

Hail helper functions

Helper functions for posting to Slack. Submit along with slack_creds.py (e.g. in HAIL_SCRIPTS environment variable in pyhail.py) which has only a slack_token variable with a Slack API key.

Submission script for Hail. Notable differences from cloudtools include:

• Inline scripts (--inline "print hc.read('gs://bucket/my.vds').count()")
• Add helper scripts designated in HAIL_SCRIPTS environment variable

Google Cloud initialization scripts. Cluster should be started up with --init gs://gnomad-public/tools/inits/master-init.sh, which is tracked here, deployed to cloud for usage. gnomad-init.sh and sparklyr-init.sh are pulled from this repo and called by master-init.sh.

Tests are run automatically on creation of each cluster (in gnomad-init.sh) and can be triggered manually using:

cd /path/to/gnomad_hail
PYTHONPATH=.:$PYTHONPATH python -m unittest discover